Starting phenix.real_space_refine
on Fri Sep 11 04:04:37 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, restraint, /net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2026/5h1b_9566.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4557      2.51       5
     N    1287      2.21       5
     O    1455      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7359
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2361
          Classifications: {'peptide': 308}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.70, per 1000 atoms: 0.23
  Number of scatterers: 7359
  At special positions: 0
  Unit cell: (107.092, 69.218, 116.234, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      18     15.00
     Mg      3     11.99
     O    1455      8.00
     N    1287      7.00
     C    4557      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 316.8 milliseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1686

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      54.1% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 28
    Processing helix  chain 'A' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU A  43 " --> pdb=" O   LYS A  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 54
      removed outlier: 4.068A  pdb=" N   VAL A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 145 through 146
      No H-bonds generated for 'chain 'A' and resid 145 through 146'
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 181 through 188
      removed outlier: 3.717A  pdb=" N   ASN A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A 214 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   MET A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU B  43 " --> pdb=" O   LYS B  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 54
      removed outlier: 4.068A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 62
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 89 through 99
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 132 through 144
    Processing helix  chain 'B' and resid 145 through 146
      No H-bonds generated for 'chain 'B' and resid 145 through 146'
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
    Processing helix  chain 'B' and resid 181 through 188
      removed outlier: 3.716A  pdb=" N   ASN B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER B 214 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 28
    Processing helix  chain 'C' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL C  38 " --> pdb=" O   ASN C  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU C  43 " --> pdb=" O   LYS C  39 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY C  45 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 54
      removed outlier: 4.067A  pdb=" N   VAL C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 62
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 132 through 144
    Processing helix  chain 'C' and resid 145 through 146
      No H-bonds generated for 'chain 'C' and resid 145 through 146'
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
    Processing helix  chain 'C' and resid 181 through 188
      removed outlier: 3.716A  pdb=" N   ASN C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR C 201 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU C 213 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C 214 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.973A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET C 251 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE C 292 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 327
      removed outlier: 8.173A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU A 124 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A 302 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   PHE A 126 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS A 304 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR A 123 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN A 267 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET A 125 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS A 156 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A 219 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 192 " --> pdb=" O   TYR A 159 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP A 161 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 193
      removed outlier: 3.717A  pdb=" N   ALA B 192 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASP B 161 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS B 156 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 219 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL B 221 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE B 160 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR B 123 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN B 267 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET B 125 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LEU B 300 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 302 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE B 126 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS B 304 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 193
      removed outlier: 3.717A  pdb=" N   ALA C 192 " --> pdb=" O   TYR C 159 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP C 161 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU C 219 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL C 221 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR C 123 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN C 267 " --> pdb=" O   THR C 123 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   MET C 125 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   LEU C 300 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU C 124 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU C 302 " --> pdb=" O   GLU C 124 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE C 126 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS C 304 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 330

    334 hydrogen bonds defined for protein.
    918 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.81

  Time building geometry restraints manager: 0.70 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2372
        1.33 -     1.45: 1159
        1.45 -     1.57: 3854
        1.57 -     1.69: 33
        1.69 -     1.81: 63
  Bond restraints: 7481
  Sorted by residual:
  bond pdb=" O3A ANP A 600 "
       pdb=" PB  ANP A 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" O3A ANP B 600 "
       pdb=" PB  ANP B 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.63e+01
  bond pdb=" O3A ANP C 600 "
       pdb=" PB  ANP C 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.60e+01
  bond pdb=" N3B ANP C 600 "
       pdb=" PG  ANP C 600 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" N3B ANP A 600 "
       pdb=" PG  ANP A 600 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.80e+01
  ... (remaining 7476 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 9923
        3.75 -     7.51: 204
        7.51 -    11.26: 15
       11.26 -    15.01: 0
       15.01 -    18.77: 3
  Bond angle restraints: 10145
  Sorted by residual:
  angle pdb=" PB  ANP C 600 "
        pdb=" N3B ANP C 600 "
        pdb=" PG  ANP C 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.18   18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" PB  ANP B 600 "
        pdb=" N3B ANP B 600 "
        pdb=" PG  ANP B 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.18   18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" PB  ANP A 600 "
        pdb=" N3B ANP A 600 "
        pdb=" PG  ANP A 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.20   18.75 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" N   THR A 197 "
        pdb=" CA  THR A 197 "
        pdb=" C   THR A 197 "
      ideal   model   delta    sigma   weight residual
     111.71  105.46    6.25 1.15e+00 7.56e-01 2.95e+01
  angle pdb=" N   THR B 197 "
        pdb=" CA  THR B 197 "
        pdb=" C   THR B 197 "
      ideal   model   delta    sigma   weight residual
     111.71  105.47    6.24 1.15e+00 7.56e-01 2.94e+01
  ... (remaining 10140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 4298
       23.74 -    47.48: 138
       47.48 -    71.22: 28
       71.22 -    94.96: 9
       94.96 -   118.70: 3
  Dihedral angle restraints: 4476
    sinusoidal: 1842
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CA  CYS C 319 "
           pdb=" C   CYS C 319 "
           pdb=" N   LEU C 320 "
           pdb=" CA  LEU C 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  CYS B 319 "
           pdb=" C   CYS B 319 "
           pdb=" N   LEU B 320 "
           pdb=" CA  LEU B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  CYS A 319 "
           pdb=" C   CYS A 319 "
           pdb=" N   LEU A 320 "
           pdb=" CA  LEU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.99  -23.01     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 4473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 882
       0.064 -    0.129: 248
       0.129 -    0.193: 25
       0.193 -    0.257: 0
       0.257 -    0.321: 3
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" C3' ANP C 600 "
            pdb=" C2' ANP C 600 "
            pdb=" C4' ANP C 600 "
            pdb=" O3' ANP C 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" C3' ANP B 600 "
            pdb=" C2' ANP B 600 "
            pdb=" C4' ANP B 600 "
            pdb=" O3' ANP B 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C3' ANP A 600 "
            pdb=" C2' ANP A 600 "
            pdb=" C4' ANP A 600 "
            pdb=" O3' ANP A 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.67    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 1155 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 246 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   ALA A 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A 247 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 246 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.06e+00
        pdb=" C   ALA B 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA B 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG B 247 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 246 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.00e+00
        pdb=" C   ALA C 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA C 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG C 247 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 46
        2.18 -     2.86: 3020
        2.86 -     3.54: 11307
        3.54 -     4.22: 18610
        4.22 -     4.90: 29872
  Nonbonded interactions: 62855
  Sorted by model distance:
  nonbonded pdb=" CB  ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.503 3.460
  nonbonded pdb=" CA  ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.572 3.470
  nonbonded pdb=" N   ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.580 3.120
  nonbonded pdb=" OH  TYR B 159 "
            pdb=" OD2 ASP B 222 "
     model   vdw
     1.586 3.040
  nonbonded pdb=" OH  TYR A 159 "
            pdb=" OD2 ASP A 222 "
     model   vdw
     1.586 3.040
  ... (remaining 62850 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.200
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.150   7484  Z= 0.691
  Angle     :  1.413  18.767  10145  Z= 0.931
  Chirality :  0.056   0.321   1158
  Planarity :  0.005   0.034   1272
  Dihedral  : 13.445 118.695   2790
  Min Nonbonded Distance : 1.503

Molprobity Statistics.
  All-atom Clashscore : 54.25
  Ramachandran Plot:
    Outliers :  2.63 %
    Allowed  :  6.25 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  :  2.43 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.27), residues: 912
  helix: -2.43 (0.18), residues: 378
  sheet: -0.80 (0.40), residues: 159
  loop :  0.92 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG C 215 
 TYR   0.019   0.002   TYR A 315 
 PHE   0.018   0.003   PHE C  86 
 HIS   0.009   0.002   HIS C 138 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01015 /  0.62 ( 7481)
  covalent geometry    : angle       1.41262 /  0.93 (10145)
  hydrogen bonds       : bond        0.21876 / 14.57 (  334)
  hydrogen bonds       : angle      10.51666 /  7.27 (  918)
  Misc. bond           : bond        0.14875 /  9.33 (    3)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6300 (mp)
REVERT: A  265 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8383 (mm)
REVERT: B   62 ASN cc_start: 0.7700 (m-40) cc_final: 0.7437 (m110)
REVERT: B   99 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6452 (mp)
REVERT: B  170 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6647 (mpt180)
REVERT: B  265 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8016 (mm)
  outliers start: 42
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1198
  time to fit residues: 19.6639
Evaluate side-chains
  70 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    5.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 138 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  93 HIS
C 138 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.039775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.034376 restraints weight = 52554.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.035492 restraints weight = 28876.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.036308 restraints weight = 18148.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.036868 restraints weight = 12350.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.037259 restraints weight = 9041.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   7484  Z= 0.270
  Angle     :  0.839   7.729  10145  Z= 0.452
  Chirality :  0.046   0.186   1158
  Planarity :  0.006   0.042   1272
  Dihedral  : 12.898 119.809   1107
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.93 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  0.54 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.27), residues: 912
  helix: -0.73 (0.22), residues: 429
  sheet: -1.11 (0.38), residues: 165
  loop :  0.29 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 170 
 TYR   0.020   0.002   TYR B 205 
 PHE   0.029   0.003   PHE A 126 
 HIS   0.006   0.002   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00568 /  0.27 ( 7481)
  covalent geometry    : angle       0.83875 /  0.45 (10145)
  hydrogen bonds       : bond        0.05723 /  3.78 (  334)
  hydrogen bonds       : angle       6.43323 /  4.46 (  918)
  Misc. bond           : bond        0.00109 /  0.07 (    3)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8786 (m-40) cc_final: 0.8391 (m110)
REVERT: A  137 CYS cc_start: 0.9021 (m) cc_final: 0.8761 (m)
REVERT: B   31 CYS cc_start: 0.6475 (t) cc_final: 0.6222 (t)
REVERT: B   62 ASN cc_start: 0.8775 (m-40) cc_final: 0.8285 (m110)
REVERT: B  248 PHE cc_start: 0.9432 (t80) cc_final: 0.9172 (t80)
REVERT: B  251 MET cc_start: 0.9164 (tpt) cc_final: 0.8882 (tpt)
REVERT: C   62 ASN cc_start: 0.8760 (m-40) cc_final: 0.8447 (m110)
REVERT: C  195 PHE cc_start: 0.7359 (p90) cc_final: 0.7082 (m-80)
REVERT: C  251 MET cc_start: 0.9159 (tpt) cc_final: 0.8698 (tpt)
REVERT: C  301 TYR cc_start: 0.8954 (t80) cc_final: 0.8676 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0849
  time to fit residues: 8.1282
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0270
   chunk 41 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    4.2046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 199 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.039209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.034147 restraints weight = 52010.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.035218 restraints weight = 28484.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.035991 restraints weight = 17912.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036482 restraints weight = 12262.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.036847 restraints weight = 9141.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7484  Z= 0.214
  Angle     :  0.726   7.878  10145  Z= 0.392
  Chirality :  0.042   0.174   1158
  Planarity :  0.005   0.067   1272
  Dihedral  : 12.556 116.318   1107
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.93 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.02 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.27), residues: 912
  helix:  0.15 (0.23), residues: 447
  sheet: -1.15 (0.40), residues: 156
  loop : -0.16 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  96 
 TYR   0.025   0.002   TYR C 315 
 PHE   0.019   0.002   PHE B 126 
 HIS   0.004   0.001   HIS A 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.21 ( 7481)
  covalent geometry    : angle       0.72588 /  0.39 (10145)
  hydrogen bonds       : bond        0.04803 /  3.20 (  334)
  hydrogen bonds       : angle       5.82217 /  4.01 (  918)
  Misc. bond           : bond        0.00096 /  0.07 (    3)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8754 (m-40) cc_final: 0.8380 (m110)
REVERT: A  137 CYS cc_start: 0.9008 (m) cc_final: 0.8721 (m)
REVERT: A  251 MET cc_start: 0.9038 (tpt) cc_final: 0.8307 (tpt)
REVERT: B   62 ASN cc_start: 0.8740 (m-40) cc_final: 0.8370 (m110)
REVERT: B  158 MET cc_start: 0.8072 (ptp) cc_final: 0.7650 (pmm)
REVERT: B  248 PHE cc_start: 0.9360 (t80) cc_final: 0.9153 (t80)
REVERT: B  251 MET cc_start: 0.9111 (tpt) cc_final: 0.8815 (tpt)
REVERT: C   62 ASN cc_start: 0.8739 (m-40) cc_final: 0.8464 (m110)
REVERT: C  195 PHE cc_start: 0.7399 (p90) cc_final: 0.7143 (m-10)
REVERT: C  225 THR cc_start: 0.9358 (p) cc_final: 0.8829 (p)
REVERT: C  243 MET cc_start: 0.8547 (tmm) cc_final: 0.8311 (tmm)
REVERT: C  251 MET cc_start: 0.9029 (tpt) cc_final: 0.8541 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0676
  time to fit residues: 6.4616
Evaluate side-chains
  42 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    2.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.039215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.033938 restraints weight = 54138.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.035038 restraints weight = 29917.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.035791 restraints weight = 18965.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.036323 restraints weight = 13204.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.036732 restraints weight = 9867.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7484  Z= 0.152
  Angle     :  0.652   7.975  10145  Z= 0.347
  Chirality :  0.040   0.155   1158
  Planarity :  0.004   0.064   1272
  Dihedral  : 12.348 112.031   1107
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.82 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.83 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.27), residues: 912
  helix:  0.63 (0.24), residues: 447
  sheet: -1.19 (0.38), residues: 165
  loop : -0.09 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 193 
 TYR   0.019   0.001   TYR C 315 
 PHE   0.011   0.002   PHE A 126 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 ( 7481)
  covalent geometry    : angle       0.65164 /  0.35 (10145)
  hydrogen bonds       : bond        0.04246 /  2.82 (  334)
  hydrogen bonds       : angle       5.38834 /  3.68 (  918)
  Misc. bond           : bond        0.00093 /  0.06 (    3)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8581 (m-40) cc_final: 0.8188 (m110)
REVERT: A  137 CYS cc_start: 0.9135 (m) cc_final: 0.8899 (m)
REVERT: B   62 ASN cc_start: 0.8695 (m-40) cc_final: 0.8311 (m110)
REVERT: B  243 MET cc_start: 0.8587 (tmm) cc_final: 0.8338 (tmm)
REVERT: B  248 PHE cc_start: 0.9359 (t80) cc_final: 0.8877 (t80)
REVERT: B  267 ASN cc_start: 0.8626 (p0) cc_final: 0.8369 (p0)
REVERT: C   62 ASN cc_start: 0.8781 (m-40) cc_final: 0.8425 (p0)
REVERT: C  137 CYS cc_start: 0.9149 (m) cc_final: 0.8915 (m)
REVERT: C  251 MET cc_start: 0.8960 (tpt) cc_final: 0.8719 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0677
  time to fit residues: 5.8775
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 58 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   chunk 62 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0470
   chunk 34 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    2.9484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 135 GLN
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 135 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.039287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.034094 restraints weight = 53003.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.035171 restraints weight = 29316.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.035940 restraints weight = 18461.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036434 restraints weight = 12726.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.036832 restraints weight = 9525.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.5186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7484  Z= 0.164
  Angle     :  0.647   7.751  10145  Z= 0.343
  Chirality :  0.039   0.154   1158
  Planarity :  0.003   0.058   1272
  Dihedral  : 12.315 110.402   1107
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.93 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.08 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.27), residues: 912
  helix:  0.80 (0.24), residues: 447
  sheet: -1.21 (0.37), residues: 165
  loop : -0.12 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 229 
 TYR   0.017   0.001   TYR B 315 
 PHE   0.025   0.002   PHE C  86 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 ( 7481)
  covalent geometry    : angle       0.64727 /  0.34 (10145)
  hydrogen bonds       : bond        0.04274 /  2.87 (  334)
  hydrogen bonds       : angle       5.29227 /  3.60 (  918)
  Misc. bond           : bond        0.00092 /  0.06 (    3)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8537 (m-40) cc_final: 0.8146 (m110)
REVERT: A  137 CYS cc_start: 0.9149 (m) cc_final: 0.8859 (m)
REVERT: A  251 MET cc_start: 0.8979 (tpt) cc_final: 0.8514 (tpt)
REVERT: B   62 ASN cc_start: 0.8671 (m-40) cc_final: 0.8324 (m110)
REVERT: B   99 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7630 (mp)
REVERT: B  243 MET cc_start: 0.8601 (tmm) cc_final: 0.8394 (tmm)
REVERT: B  248 PHE cc_start: 0.9364 (t80) cc_final: 0.9014 (t80)
REVERT: B  267 ASN cc_start: 0.8621 (p0) cc_final: 0.8307 (p0)
REVERT: C   62 ASN cc_start: 0.8791 (m-40) cc_final: 0.8445 (p0)
REVERT: C  137 CYS cc_start: 0.9154 (m) cc_final: 0.8872 (m)
REVERT: C  251 MET cc_start: 0.8953 (tpt) cc_final: 0.8691 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0709
  time to fit residues: 6.2107
Evaluate side-chains
  42 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 135 GLN
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.040242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.035192 restraints weight = 51958.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.036292 restraints weight = 28480.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.037050 restraints weight = 17901.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.037591 restraints weight = 12352.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.037872 restraints weight = 9063.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.5484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7484  Z= 0.126
  Angle     :  0.636  11.300  10145  Z= 0.328
  Chirality :  0.039   0.184   1158
  Planarity :  0.003   0.049   1272
  Dihedral  : 12.153 109.186   1107
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.28 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.27), residues: 912
  helix:  1.11 (0.24), residues: 447
  sheet: -0.92 (0.40), residues: 147
  loop : -0.24 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 229 
 TYR   0.008   0.001   TYR C 216 
 PHE   0.034   0.002   PHE B  86 
 HIS   0.003   0.001   HIS B 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.13 ( 7481)
  covalent geometry    : angle       0.63621 /  0.33 (10145)
  hydrogen bonds       : bond        0.03986 /  2.65 (  334)
  hydrogen bonds       : angle       5.09287 /  3.46 (  918)
  Misc. bond           : bond        0.00054 /  0.04 (    3)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.9088 (pttp) cc_final: 0.8680 (ptpt)
REVERT: A   62 ASN cc_start: 0.8544 (m-40) cc_final: 0.8155 (m110)
REVERT: A  137 CYS cc_start: 0.9197 (m) cc_final: 0.8969 (m)
REVERT: A  251 MET cc_start: 0.8918 (tpt) cc_final: 0.8441 (tpt)
REVERT: B   62 ASN cc_start: 0.8648 (m-40) cc_final: 0.8306 (m110)
REVERT: B   84 MET cc_start: 0.7891 (mmm) cc_final: 0.7670 (mmm)
REVERT: B  137 CYS cc_start: 0.9218 (m) cc_final: 0.9017 (m)
REVERT: B  248 PHE cc_start: 0.9378 (t80) cc_final: 0.9044 (t80)
REVERT: B  267 ASN cc_start: 0.8632 (p0) cc_final: 0.8345 (p0)
REVERT: C   62 ASN cc_start: 0.8779 (m-40) cc_final: 0.8462 (p0)
REVERT: C  137 CYS cc_start: 0.9167 (m) cc_final: 0.8930 (m)
REVERT: C  206 GLN cc_start: 0.9023 (mt0) cc_final: 0.8738 (tt0)
REVERT: C  251 MET cc_start: 0.8931 (tpt) cc_final: 0.8666 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0737
  time to fit residues: 6.3661
Evaluate side-chains
  44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 72 optimal weight:    0.3980
   chunk 47 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    3.6788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.039058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.033881 restraints weight = 54900.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.034925 restraints weight = 30579.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.035666 restraints weight = 19516.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.036123 restraints weight = 13573.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.036492 restraints weight = 10395.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.5631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7484  Z= 0.181
  Angle     :  0.671   8.703  10145  Z= 0.348
  Chirality :  0.040   0.193   1158
  Planarity :  0.003   0.053   1272
  Dihedral  : 12.260 110.772   1107
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.71 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.27), residues: 912
  helix:  1.11 (0.24), residues: 447
  sheet: -0.79 (0.40), residues: 147
  loop : -0.29 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  96 
 TYR   0.010   0.001   TYR B 216 
 PHE   0.023   0.002   PHE B  86 
 HIS   0.003   0.001   HIS A 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.18 ( 7481)
  covalent geometry    : angle       0.67142 /  0.35 (10145)
  hydrogen bonds       : bond        0.04085 /  2.75 (  334)
  hydrogen bonds       : angle       5.14863 /  3.51 (  918)
  Misc. bond           : bond        0.00114 /  0.08 (    3)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8594 (m-40) cc_final: 0.8225 (m110)
REVERT: A  137 CYS cc_start: 0.9139 (m) cc_final: 0.8894 (m)
REVERT: A  158 MET cc_start: 0.8507 (pmm) cc_final: 0.8189 (pmm)
REVERT: A  251 MET cc_start: 0.8943 (tpt) cc_final: 0.8408 (tpt)
REVERT: B   62 ASN cc_start: 0.8649 (m-40) cc_final: 0.8258 (m110)
REVERT: B  137 CYS cc_start: 0.9253 (m) cc_final: 0.9004 (m)
REVERT: B  248 PHE cc_start: 0.9404 (t80) cc_final: 0.9023 (t80)
REVERT: B  267 ASN cc_start: 0.8680 (p0) cc_final: 0.8455 (p0)
REVERT: C   62 ASN cc_start: 0.8772 (m-40) cc_final: 0.8469 (p0)
REVERT: C  137 CYS cc_start: 0.9189 (m) cc_final: 0.8947 (m)
REVERT: C  206 GLN cc_start: 0.9076 (mt0) cc_final: 0.8697 (tt0)
REVERT: C  211 MET cc_start: 0.8539 (mmt) cc_final: 0.8336 (mmp)
REVERT: C  251 MET cc_start: 0.8956 (tpt) cc_final: 0.8441 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0662
  time to fit residues: 5.2683
Evaluate side-chains
  41 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 59 optimal weight:   20.0000
   chunk 61 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.039015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.034039 restraints weight = 55311.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.035092 restraints weight = 30342.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.035811 restraints weight = 19076.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.036342 restraints weight = 13256.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036684 restraints weight = 9805.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.5772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7484  Z= 0.198
  Angle     :  0.678   8.479  10145  Z= 0.351
  Chirality :  0.040   0.168   1158
  Planarity :  0.004   0.048   1272
  Dihedral  : 12.324 109.769   1107
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  4.71 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.27), residues: 912
  helix:  1.11 (0.24), residues: 447
  sheet: -0.81 (0.42), residues: 141
  loop : -0.36 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  96 
 TYR   0.009   0.001   TYR B 315 
 PHE   0.025   0.002   PHE B  86 
 HIS   0.003   0.001   HIS A 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.20 ( 7481)
  covalent geometry    : angle       0.67811 /  0.35 (10145)
  hydrogen bonds       : bond        0.04075 /  2.72 (  334)
  hydrogen bonds       : angle       5.15321 /  3.52 (  918)
  Misc. bond           : bond        0.00133 /  0.09 (    3)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8585 (m-40) cc_final: 0.8213 (m110)
REVERT: A  137 CYS cc_start: 0.9200 (m) cc_final: 0.8990 (m)
REVERT: A  251 MET cc_start: 0.8957 (tpt) cc_final: 0.8444 (tpt)
REVERT: B   62 ASN cc_start: 0.8664 (m-40) cc_final: 0.8284 (m110)
REVERT: B  137 CYS cc_start: 0.9294 (m) cc_final: 0.9063 (m)
REVERT: B  158 MET cc_start: 0.7822 (mpp) cc_final: 0.7462 (mpp)
REVERT: B  243 MET cc_start: 0.8400 (tmm) cc_final: 0.8164 (tmm)
REVERT: B  248 PHE cc_start: 0.9394 (t80) cc_final: 0.9027 (t80)
REVERT: B  267 ASN cc_start: 0.8661 (p0) cc_final: 0.8397 (p0)
REVERT: C   62 ASN cc_start: 0.8781 (m-40) cc_final: 0.8500 (p0)
REVERT: C  137 CYS cc_start: 0.9205 (m) cc_final: 0.8966 (m)
REVERT: C  206 GLN cc_start: 0.9089 (mt0) cc_final: 0.8676 (tt0)
REVERT: C  251 MET cc_start: 0.8975 (tpt) cc_final: 0.8435 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0668
  time to fit residues: 5.3059
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  47 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.033993 restraints weight = 54440.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.035047 restraints weight = 30124.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.035772 restraints weight = 19065.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.036299 restraints weight = 13260.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.036631 restraints weight = 9839.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.5905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7484  Z= 0.205
  Angle     :  0.699   8.214  10145  Z= 0.359
  Chirality :  0.041   0.181   1158
  Planarity :  0.004   0.043   1272
  Dihedral  : 12.310 107.185   1107
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.82 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.28), residues: 912
  helix:  1.13 (0.24), residues: 447
  sheet: -0.77 (0.43), residues: 141
  loop : -0.45 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  96 
 TYR   0.011   0.001   TYR C 315 
 PHE   0.024   0.002   PHE B  86 
 HIS   0.003   0.001   HIS A 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.20 ( 7481)
  covalent geometry    : angle       0.69878 /  0.36 (10145)
  hydrogen bonds       : bond        0.04075 /  2.72 (  334)
  hydrogen bonds       : angle       5.15926 /  3.52 (  918)
  Misc. bond           : bond        0.00125 /  0.09 (    3)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8583 (m-40) cc_final: 0.8217 (m110)
REVERT: A  137 CYS cc_start: 0.9180 (m) cc_final: 0.8979 (m)
REVERT: A  251 MET cc_start: 0.8941 (tpt) cc_final: 0.8474 (tpt)
REVERT: B   62 ASN cc_start: 0.8712 (m-40) cc_final: 0.8382 (m110)
REVERT: B  137 CYS cc_start: 0.9257 (m) cc_final: 0.8994 (m)
REVERT: B  158 MET cc_start: 0.7889 (mpp) cc_final: 0.7569 (mpp)
REVERT: B  243 MET cc_start: 0.8419 (tmm) cc_final: 0.8159 (tmm)
REVERT: B  248 PHE cc_start: 0.9419 (t80) cc_final: 0.9065 (t80)
REVERT: B  267 ASN cc_start: 0.8620 (p0) cc_final: 0.8400 (p0)
REVERT: C   62 ASN cc_start: 0.8789 (m-40) cc_final: 0.8506 (p0)
REVERT: C  137 CYS cc_start: 0.9210 (m) cc_final: 0.8970 (m)
REVERT: C  251 MET cc_start: 0.8967 (tpt) cc_final: 0.8506 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0671
  time to fit residues: 5.1500
Evaluate side-chains
  42 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   chunk 86 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 58 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 ASN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.040086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.035066 restraints weight = 53381.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036174 restraints weight = 29512.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.036920 restraints weight = 18740.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.037446 restraints weight = 13000.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.037825 restraints weight = 9594.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7484  Z= 0.126
  Angle     :  0.671   8.703  10145  Z= 0.337
  Chirality :  0.040   0.171   1158
  Planarity :  0.003   0.038   1272
  Dihedral  : 12.007 101.843   1107
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.17 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.27 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.28), residues: 912
  helix:  1.29 (0.24), residues: 447
  sheet: -0.77 (0.44), residues: 141
  loop : -0.42 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 299 
 TYR   0.010   0.001   TYR C 216 
 PHE   0.017   0.001   PHE B  86 
 HIS   0.002   0.001   HIS A 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.13 ( 7481)
  covalent geometry    : angle       0.67109 /  0.34 (10145)
  hydrogen bonds       : bond        0.03745 /  2.49 (  334)
  hydrogen bonds       : angle       4.93022 /  3.37 (  918)
  Misc. bond           : bond        0.00054 /  0.04 (    3)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8777 (pttp) cc_final: 0.8294 (ptpt)
REVERT: A   62 ASN cc_start: 0.8595 (m-40) cc_final: 0.8278 (m110)
REVERT: A  251 MET cc_start: 0.8901 (tpt) cc_final: 0.8340 (tpt)
REVERT: B   62 ASN cc_start: 0.8692 (m-40) cc_final: 0.8301 (m110)
REVERT: B  137 CYS cc_start: 0.9255 (m) cc_final: 0.9045 (m)
REVERT: B  243 MET cc_start: 0.8326 (tmm) cc_final: 0.8035 (tmm)
REVERT: B  248 PHE cc_start: 0.9417 (t80) cc_final: 0.9057 (t80)
REVERT: B  267 ASN cc_start: 0.8479 (p0) cc_final: 0.8251 (p0)
REVERT: C   62 ASN cc_start: 0.8710 (m-40) cc_final: 0.8426 (p0)
REVERT: C  137 CYS cc_start: 0.9139 (m) cc_final: 0.8907 (m)
REVERT: C  251 MET cc_start: 0.8946 (tpt) cc_final: 0.8409 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 57
  average time/residue: 0.0752
  time to fit residues: 6.0506
Evaluate side-chains
  43 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    3.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.039352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.034304 restraints weight = 54554.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.035369 restraints weight = 30504.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.036098 restraints weight = 19348.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.036656 restraints weight = 13318.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.037001 restraints weight = 9863.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.6224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7484  Z= 0.190
  Angle     :  0.713   8.914  10145  Z= 0.359
  Chirality :  0.040   0.168   1158
  Planarity :  0.004   0.039   1272
  Dihedral  : 12.129 102.966   1107
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  5.04 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.28), residues: 912
  helix:  1.37 (0.24), residues: 429
  sheet: -0.80 (0.44), residues: 138
  loop : -0.29 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  96 
 TYR   0.013   0.001   TYR C 315 
 PHE   0.023   0.002   PHE B  86 
 HIS   0.003   0.001   HIS A 294 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.19 ( 7481)
  covalent geometry    : angle       0.71336 /  0.36 (10145)
  hydrogen bonds       : bond        0.03976 /  2.61 (  334)
  hydrogen bonds       : angle       5.09529 /  3.49 (  918)
  Misc. bond           : bond        0.00114 /  0.08 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 933.37 seconds
wall clock time: 17 minutes 2.15 seconds (1022.15 seconds total)